view tools/filters/gff/gff_filter_by_feature_count.xml @ 0:9071e359b9a3

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<tool id="gff_filter_by_feature_count" name="Filter GFF data by feature count" version="0.1">
  <description>using simple expressions</description>
  <command interpreter="python">
    gff_filter_by_feature_count.py $input_file1 $out_file1 "$feature_name" "$cond"
  </command>
  <inputs>
    <param format="gff" name="input_file1" type="data" label="Filter"/>
    <param name="feature_name" type="select" label="Using feature name">
        <options from_dataset="input_file1">
            <column name="name" index="2"/>
            <column name="value" index="2"/>
            <filter type="unique_value" name="unique" column="2"/>
        </options>
    </param>
    <param name="cond" size="40" type="text" value=">0" label="With following condition">
      <validator type="empty_field" message="Enter a valid filtering condition, see syntax and examples below."/>
    </param>
  </inputs>
  <outputs>
    <data format="input" name="out_file1" metadata_source="input_file1"/>
  </outputs>
  <tests>
      <!-- Test GTF filtering. -->
      <test>
          <param name="input_file1" value="gops_subtract_in1.gff"/>
          <param name="feature_name" value="exon"/>
          <param name="cond" value=">1"/>
          <output name="out_file1" file="gff_filter_by_feature_count_out1.gff"/>
      </test>
      <!-- Test GFF3 filtering. -->
      <test>
          <param name="input_file1" value="5.gff3"/>
          <param name="feature_name" value="HSP"/>
          <param name="cond" value=">=5"/>
          <output name="out_file1" file="gff_filter_by_feature_count_out2.gff"/>
      </test>
  </tests>

  <help>


.. class:: infomark

Valid comparison operators are: &gt; &lt; &gt;=, &lt;=, !=, and ==

-----

**Syntax**

The filter tool allows you to restrict the dataset based on transcripts' feature counts.

</help>
</tool>